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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Repetitive Sequences, Nucleic Acid

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Disease relevance of Repetitive Sequences, Nucleic Acid

  • Recombination between the IS50 sequences that flank Tn5 has been found to occur readily after the transformation of E. coli recA strains with a plasmid that contains direct repeats of these sequences [1].
  • Two different Xho I linker insertion mutants of the herpes simplex virus type 1 thymidine kinase (HTK) gene were introduced into mouse LTK- cells as direct repeats on a plasmid carrying a dominant selectable marker [2].
  • The entire genome of this prophage, named phi R73, is 12.7 kilobase pairs and is flanked by 29-base pair direct repeats derived from the 3' end of the selenocystyl transfer RNA gene (selC) [3].
  • Crucial to the lysis/lysogeny decision is the homotetrameric transcription-activator protein CII (4 x 11 kDa) of the phage that binds to a unique direct-repeat sequence T-T-G-C-N6-T-T-G-C at each of the three phage promoters it activates: p(E), p(I), and p(aQ) [4].
  • It appears that the genetic domain of glucocorticoid control in M1.19 rat hepatoma cells involves low copy number genes such as alpha 1-acid glycoprotein as well as repetitive sequence elements [5].

High impact information on Repetitive Sequences, Nucleic Acid

  • Instead of an inverted repeat (CANNTG), the target for all known bHLH-ZIP proteins, SRE-1 contains a direct repeat of CAC [6].
  • Here we show that the human homologue of the murine pmp-22 gene is located within the CMT1A DNA duplication, which is a direct repeat and does not interrupt the coding region of PMP-22 [7].
  • RARE1 and RARE2 are direct repeats (DR) of two motifs separated by 2 bp (DR2) and 1 bp (DR1), respectively, and bind RAR-RXR heterodimers more efficiently than homodimers [8].
  • A direct repeat in the cellular retinol-binding protein type II gene confers differential regulation by RXR and RAR [9].
  • Unlike palindromic TREs, direct repeat TREs do not confer a retinoic acid response [10].

Chemical compound and disease context of Repetitive Sequences, Nucleic Acid


Biological context of Repetitive Sequences, Nucleic Acid


Anatomical context of Repetitive Sequences, Nucleic Acid


Associations of Repetitive Sequences, Nucleic Acid with chemical compounds

  • Distamycin appeared to antagonize the binding of the initiator to the seven 22 bp direct repeats [26].
  • RXR homodimers activate transcription in response to 9-cis retinoic acid by binding to direct repeats spaced by one base pair (DR1 elements) [27].
  • The insert was flanked by an 8-bp direct repeat reminiscent of a transposable element, and appeared to code for a region of marked structural homology to the NH2-terminal region of the receptor molecule [28].
  • Here we identify GARPs as multivalent proteins that interact with the key players of cGMP signalling, phosphodiesterase and guanylate cyclase, and with a retina-specific ATP-binding cassette transporter (ABCR), through four, short, repetitive sequences [29].
  • We present evidence that the preference for direct repeat elements arises from two fundamental differences from steroid hormone receptors [30].

Gene context of Repetitive Sequences, Nucleic Acid

  • The molecular analysis of the NSP1 protein points to a two domain model: a nonessential domain (the first 603 amino acids) composed of repetitive sequences common to other nuclear proteins and an essential, carboxy-terminal domain (residues 604-823) mediating the vital function of NSP1 [31].
  • Sites with inverted CGGs were not recovered, and mutations converting the direct repeat of CGGs to an inverted repeat greatly reduce HAP1-binding affinity [32].
  • A 51-bp distal element PB-responsive enhancer module (PBREM) conserved in the PB-inducible CYP2B genes contains two NR-binding direct repeat (DR)-4 motifs [33].
  • The combined data strongly suggest that numerous recombination events are restricted to the initiation side of the microsatellite as though progression of the strand exchange initiated at the ARG4 promoter locus was impaired by the repetitive sequence [34].
  • Moreover, substitution of the HAP1 dimerization domain with that of PPR1, which forms coiled-coils and dimerizes symmetrically, did not diminish the ability of the protein to bind selectively to a direct repeat [32].

Analytical, diagnostic and therapeutic context of Repetitive Sequences, Nucleic Acid


  1. RecA-independent recombination between direct repeats of IS50. Zupancic, T.J., Marvo, S.L., Chung, J.H., Peralta, E.G., Jaskunas, S.R. Cell (1983) [Pubmed]
  2. Evidence for intrachromosomal gene conversion in cultured mouse cells. Liskay, R.M., Stachelek, J.L. Cell (1983) [Pubmed]
  3. Retronphage phi R73: an E. coli phage that contains a retroelement and integrates into a tRNA gene. Inouye, S., Sunshine, M.G., Six, E.W., Inouye, M. Science (1991) [Pubmed]
  4. Structure of lambda CII: implications for recognition of direct-repeat DNA by an unusual tetrameric organization. Datta, A.B., Panjikar, S., Weiss, M.S., Chakrabarti, P., Parrack, P. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  5. Identification of glucocorticoid-induced genes in rat hepatoma cells by isolation of cloned cDNA sequences. Feinberg, R.F., Sun, L.H., Ordahl, C.P., Frankel, F.R. Proc. Natl. Acad. Sci. U.S.A. (1983) [Pubmed]
  6. SREBP-1, a basic-helix-loop-helix-leucine zipper protein that controls transcription of the low density lipoprotein receptor gene. Yokoyama, C., Wang, X., Briggs, M.R., Admon, A., Wu, J., Hua, X., Goldstein, J.L., Brown, M.S. Cell (1993) [Pubmed]
  7. The peripheral myelin gene PMP-22/GAS-3 is duplicated in Charcot-Marie-Tooth disease type 1A. Valentijn, L.J., Bolhuis, P.A., Zorn, I., Hoogendijk, J.E., van den Bosch, N., Hensels, G.W., Stanton, V.P., Housman, D.E., Fischbeck, K.H., Ross, D.A. Nat. Genet. (1992) [Pubmed]
  8. All-trans and 9-cis retinoic acid induction of CRABPII transcription is mediated by RAR-RXR heterodimers bound to DR1 and DR2 repeated motifs. Durand, B., Saunders, M., Leroy, P., Leid, M., Chambon, P. Cell (1992) [Pubmed]
  9. A direct repeat in the cellular retinol-binding protein type II gene confers differential regulation by RXR and RAR. Mangelsdorf, D.J., Umesono, K., Kliewer, S.A., Borgmeyer, U., Ong, E.S., Evans, R.M. Cell (1991) [Pubmed]
  10. Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors. Umesono, K., Murakami, K.K., Thompson, C.C., Evans, R.M. Cell (1991) [Pubmed]
  11. A retinoic acid response element is present in the mouse cellular retinol binding protein I (mCRBPI) promoter. Smith, W.C., Nakshatri, H., Leroy, P., Rees, J., Chambon, P. EMBO J. (1991) [Pubmed]
  12. Retinoic acid stimulates erythropoietin gene transcription in embryonal carcinoma cells through the direct repeat of a steroid/thyroid hormone receptor response element half-site in the hypoxia-response enhancer. Kambe, T., Tada-Kambe, J., Kuge, Y., Yamaguchi-Iwai, Y., Nagao, M., Sasaki, R. Blood (2000) [Pubmed]
  13. Are the PE-PGRS proteins of Mycobacterium tuberculosis variable surface antigens? Banu, S., Honoré, N., Saint-Joanis, B., Philpott, D., Prévost, M.C., Cole, S.T. Mol. Microbiol. (2002) [Pubmed]
  14. Psi- vectors: murine leukemia virus-based self-inactivating and self-activating retroviral vectors. Delviks, K.A., Hu, W.S., Pathak, V.K. J. Virol. (1997) [Pubmed]
  15. Two pathogenicity islands in uropathogenic Escherichia coli J96: cosmid cloning and sample sequencing. Swenson, D.L., Bukanov, N.O., Berg, D.E., Welch, R.A. Infect. Immun. (1996) [Pubmed]
  16. Interspersion of repetitive and nonrepetitive DNA sequences in the Drosophila melanogaster genome. Manning, J.E., Schmid, C.W., Davidson, N. Cell (1975) [Pubmed]
  17. The virD operon of Agrobacterium tumefaciens encodes a site-specific endonuclease. Yanofsky, M.F., Porter, S.G., Young, C., Albright, L.M., Gordon, M.P., Nester, E.W. Cell (1986) [Pubmed]
  18. Nucleotide sequence analysis of the chloramphenicol resistance transposon Tn9. Alton, N.K., Vapnek, D. Nature (1979) [Pubmed]
  19. Direct repeats in HSF binding sites. Raibaud, O. Nature (1990) [Pubmed]
  20. Terminal direct repeats in a retrovirus-like repeated mouse gene family. Keshet, E., Shaul, Y. Nature (1981) [Pubmed]
  21. The mouse peroxisome proliferator activated receptor recognizes a response element in the 5' flanking sequence of the rat acyl CoA oxidase gene. Tugwood, J.D., Issemann, I., Anderson, R.G., Bundell, K.R., McPheat, W.L., Green, S. EMBO J. (1992) [Pubmed]
  22. Amplification of the X-linked Drosophila chorion gene cluster requires a region upstream from the s38 chorion gene. Spradling, A.C., de Cicco, D.V., Wakimoto, B.T., Levine, J.F., Kalfayan, L.J., Cooley, L. EMBO J. (1987) [Pubmed]
  23. High-frequency intrachromosomal gene conversion induced by triplex-forming oligonucleotides microinjected into mouse cells. Luo, Z., Macris, M.A., Faruqi, A.F., Glazer, P.M. Proc. Natl. Acad. Sci. U.S.A. (2000) [Pubmed]
  24. Beyond affect: a role for genetic variation of the serotonin transporter in neural activation during a cognitive attention task. Canli, T., Omura, K., Haas, B.W., Fallgatter, A., Constable, R.T., Lesch, K.P. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  25. Replication in the amplified dihydrofolate reductase domain in CHO cells may initiate at two distinct sites, one of which is a repetitive sequence element. Anachkova, B., Hamlin, J.L. Mol. Cell. Biol. (1989) [Pubmed]
  26. Conformational changes in a replication origin induced by an initiator protein. Mukherjee, S., Patel, I., Bastia, D. Cell (1985) [Pubmed]
  27. Regulation of retinoid signalling by receptor polarity and allosteric control of ligand binding. Kurokawa, R., DiRenzo, J., Boehm, M., Sugarman, J., Gloss, B., Rosenfeld, M.G., Heyman, R.A., Glass, C.K. Nature (1994) [Pubmed]
  28. Cloning, sequence and expression of human interleukin-2 receptor. Cosman, D., Cerretti, D.P., Larsen, A., Park, L., March, C., Dower, S., Gillis, S., Urdal, D. Nature (1984) [Pubmed]
  29. Interaction of glutamic-acid-rich proteins with the cGMP signalling pathway in rod photoreceptors. Körschen, H.G., Beyermann, M., Müller, F., Heck, M., Vantler, M., Koch, K.W., Kellner, R., Wolfrum, U., Bode, C., Hofmann, K.P., Kaupp, U.B. Nature (1999) [Pubmed]
  30. Differential orientations of the DNA-binding domain and carboxy-terminal dimerization interface regulate binding site selection by nuclear receptor heterodimers. Kurokawa, R., Yu, V.C., Näär, A., Kyakumoto, S., Han, Z., Silverman, S., Rosenfeld, M.G., Glass, C.K. Genes Dev. (1993) [Pubmed]
  31. NSP1: a yeast nuclear envelope protein localized at the nuclear pores exerts its essential function by its carboxy-terminal domain. Nehrbass, U., Kern, H., Mutvei, A., Horstmann, H., Marshallsay, B., Hurt, E.C. Cell (1990) [Pubmed]
  32. The yeast activator HAP1--a GAL4 family member--binds DNA in a directly repeated orientation. Zhang, L., Guarente, L. Genes Dev. (1994) [Pubmed]
  33. Phenobarbital response elements of cytochrome P450 genes and nuclear receptors. Sueyoshi, T., Negishi, M. Annu. Rev. Pharmacol. Toxicol. (2001) [Pubmed]
  34. (CA/GT)(n) microsatellites affect homologous recombination during yeast meiosis. Gendrel, C.G., Boulet, A., Dutreix, M. Genes Dev. (2000) [Pubmed]
  35. Evolution of a human Y chromosome-specific repeated sequence. Cooke, H.J., McKay, R.D. Cell (1978) [Pubmed]
  36. Diffuse leukodystrophy with a large-scale mitochondrial DNA deletion. Nakai, A., Goto, Y., Fujisawa, K., Shigematsu, Y., Kikawa, Y., Konishi, Y., Nonaka, I., Sudo, M. Lancet (1994) [Pubmed]
  37. DNA target selectivity by the vitamin D3 receptor: mechanism of dimer binding to an asymmetric repeat element. Towers, T.L., Luisi, B.F., Asianov, A., Freedman, L.P. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  38. Molecular cloning of a novel Ca(2+)-binding protein (calmegin) specifically expressed during male meiotic germ cell development. Watanabe, D., Yamada, K., Nishina, Y., Tajima, Y., Koshimizu, U., Nagata, A., Nishimune, Y. J. Biol. Chem. (1994) [Pubmed]
  39. Thyroid hormone response elements differentially modulate the interactions of thyroid hormone receptors with two receptor binding domains in the steroid receptor coactivator-1. Takeshita, A., Yen, P.M., Ikeda, M., Cardona, G.R., Liu, Y., Koibuchi, N., Norwitz, E.R., Chin, W.W. J. Biol. Chem. (1998) [Pubmed]
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